new web

config.toml

@@ -1,6 +1,6 @@
 baseurl = "https://pliu.rbind.io/"
 title = "Peng Liu"
-copyright = "© 2017 Peng Liu"
+copyright = "© 2018 Peng Liu"
 theme = "hugo-academic"
 enableEmoji = true
 footnotereturnlinkcontents = "<sup>^</sup>"
@@ -20,8 +20,8 @@ defaultContentLanguageInSubdir = false
 [outputs]
   home = [ "HTML", "CSS" ]
 
-[blackfriday]
-  hrefTargetBlank = true
+#[blackfriday]
+#  hrefTargetBlank = true
 
 [params]
   # Color theme.
@@ -54,14 +54,14 @@ defaultContentLanguageInSubdir = false
 
   # Date format (refer to Go's date format: http://flippinggodateformat.com )
   #   Examples: "Mon, Jan 2, 2006" or "2006-01-02"
-  date_format = "Jan 2, 2018"
+  date_format = "Mon, Jan 2, 2006"
 
   # Show estimated reading time for posts?
-  reading_time = true
+  # reading_time = true
 
   # Enable global LaTeX math rendering?
   #   If false, you can enable it locally on a per page basis.
-  math = false
+  math = true
 
   # Highlight.js options
   #   highlight
@@ -95,7 +95,7 @@ defaultContentLanguageInSubdir = false
   # highlight_style = "github"
 
   # Enable native social sharing buttons?
-  sharing = true
+  # sharing = true
 
   # Link custom CSS and JS assets
   #   (relative to /static/css and /static/js respectively)
@@ -169,34 +169,44 @@ defaultContentLanguageInSubdir = false
 
 [[menu.main]]
   name = "Publications"
-  url = "#publications_selected"
+  url = "/publication/"
   weight = 2
 
-#[[menu.main]]
-#  name = "Posts"
-#  url = "#posts"
-#  weight = 3
+[[menu.main]]
+  name = "Talks"
+  url = "/talk/"
+  weight = 3
 
-#[[menu.main]]
-#  name = "Projects"
-#  url = "#projects"
-#  weight = 4
+[[menu.main]]
+  name = "Grants"
+  url = "/grant/"
+  weight = 4
 
 [[menu.main]]
   name = "Teaching"
-  url = "#teaching"
+  url = "/teaching/"
   weight = 5
 
 [[menu.main]]
-  name = "Contact"
-  url = "#contact"
+  name = "Students"
+  url = "/student/"
   weight = 6
 
+[[menu.main]]
+  name = "CV"
+  url = "/Peng_Liu_CV.pdf"
+  weight = 7
+
+[[menu.main]]
+  name = "Contact"
+  url = "/contact/"
+  weight = 8
+
 # Taxonomies.
-[taxonomies]
-  tag = "tags"
-  category = "categories"
-  publication_type = "publication_types"
+#[taxonomies]
+#  tag = "tags"
+#  category = "categories"
+#  publication_type = "publication_types"
 
 # Languages
 #   Create a [languages.X] block for each language you want, where X is the language ID.

content/contact.md

@@ -0,0 +1,18 @@
+---
+autolink: true
+date: 2018-03-20T00:00:00
+draft: false
+subtitle: ""
+title: Contact
+weight: 70
+widget: contact
+---
+
+2117 Snedecor Hall, [Department of Statistics](http://stat.iastate.edu/) \\
+[Iowa State University](http://www.iastate.edu/) \\
+Ames, IA 50011
+
+
+Phone: (515) 294-7806
+
+Email: <A HREF="mailto:pliu@iastate.edu">pliu@iastate.edu</A>

content/grant/NSF2012.md

@@ -0,0 +1,33 @@
+---
+date: "2012-02-15"
+# Grant title.
+title: "A Systems Approach to the Development and Function of C4 Photosynthesis"
+# Grant summary to display on homepage.
+summary: "Nelson Thomas, Thomas Brutnell, Klaas van Wijk, Todd Mockler, **Peng Liu**"
+# Tags: can be used for filtering projects.
+# Example: tags = ["machine-learning", "deep-learning"]
+tags: [""]
+# Does the project detail page use math formatting?
+math: false
+# Optional featured image (relative to static/img/ folder).
+header:
+  caption: "A Systems Approach to the Development and Function of C4 Photosynthesis"
+  image: ""
+---
+
+### [Abstract](http://grantome.com/grant/NSF/IOS-1127017)
+
+### PIs
+Nelson Thomas (leading PI, Yale University); Thomas Brutnell and Todd Mockler (Danforth Plant Science Center); **Peng Liu** (Iowa State University); Chris Myers, Robert Turgeon, Qi Sun, and Klaas van Wijk (Cornell University); and Joyce van Eck (Boyce Thompson Institute)
+
+### Source of Support
+[NSF](https://www.nsf.gov/)
+
+### Total Award Amount
+$ 8,386,495
+
+### My portion
+$ 372,843
+
+### Total Award Period Covered
+02/15/2012 - 01/31/2016

content/grant/_index.md

@@ -0,0 +1,11 @@
+---
+date: 2017-01-01T00:00:00Z
+header:
+  caption: ""
+  image: ""
+highlight: false
+math: false
+list_format: 1
+title: Grants
+---
+

content/home/about.md

@@ -1,22 +1,33 @@
 ---
-date: 2016-04-20T00:00:00
+# About/Biography widget.
+
+date: 2018-03-20T00:00:00
+
+# List your academic interests.
+interests:
+  interests:
+  - Statistical Genomics, Bioinformatics, Biostatistics
+  - Statistical Inference for High-dimensional Data
+  - Bayesian Statistics
+
+# List your qualifications (such as academic degrees).
 education:
   courses:
   - course: PhD in Biological Statistics and Computational Biology
     institution: Cornell University
     year: 2006
+  - course: MS in Biological Statistics and Computational Biology
+    institution: Cornell University
+    year: 2004
   - course: MS in Nutritional Sciences
     institution: Cornell University
     year: 2001
   - course: BMed (Medical Degree) in Basic Medical Sicences
     institution: Peking University Health Science Center
     year: 1998
-interests:
-  interests:
-  - Statistical Genomics, Bioinformatics, Biostatistics
-  - Statistical Inference for High-dimensional Data
-  - Bayesian Statistics
-weight: 5
+
+# Order that this section will appear in.
+weight: 1
 widget: about
 ---
 

content/publication/Frontiers2017.md

@@ -11,14 +11,17 @@ authors:
 - Michael Blanco
 - Thomas Lübberstedt
 date: 2017-06-20
+header:
+  caption: 'Gibberellins promote brassinosteroids action and both increase heterosis for plant height in maize (Zea mays L.)'
+  image: headers/bubbles-wide.jpg
 image_preview: ""
 math: true
 publication: In *Frontiers*.
 publication_short: In *Frontiers*
 publication_types:
 - "2"
 selected: false
-title: Gibberellins promote brassinosteroids action and both increase heterosis for plant height in maize (Zea mays L.)
+title: "Hu S., Wang C., Sanchez D. L., Lipka A. E., Liu P., Yin Y., et al. (2017). Gibberellins promote brassinosteroids action and both increase heterosis for plant height in maize (Zea mays L.). Front. Plant Sci. 8:1039."
 url_code: ""
 url_dataset: ""
 url_pdf: https://www.frontiersin.org/articles/10.3389/fpls.2017.01039/full

content/publication/JABES2015.md

@@ -0,0 +1,30 @@
+---
+abstract: RNA-sequencing (RNA-seq) technologies have revolutionized the way that agricultural biologists study gene expression as well as generated a tremendous amount of data waiting for analysis. Detecting differentially expressed genes is one of the fundamental steps in RNA-seq data analysis. In this paper, we model the count data from RNA-seq experiments with a Poisson–Gamma hierarchical model, or equivalently, a negative binomial model. We derive a semi-parametric Bayesian approach with a Dirichlet process as the prior model for the distribution of fold changes between the two treatment means. An inference strategy using Gibbs algorithm is developed for differential expression analysis. The results of several simulation studies show that our proposed method outperforms other methods including the popularly applied edgeR and DESeq methods. We also discuss an application of our method to a dataset that compares gene expression between bundle sheath and mesophyll cells in maize leaves. Supplementary materials accompanying this paper appear online.
+abstract_short: ""
+authors:
+- Fangfang Liu
+- Chong Wang
+- Peng Liu
+date: 2015-12-20
+header:
+  caption: 'A Semi-parametric Bayesian Approach for Differential Expression Analysis of RNA-seq Data'
+  image: headers/bubbles-wide.jpg
+image_preview: ""
+math: true
+publication: In *Journal of Agricultural, Biological, and Environmental Statistics*.
+publication_short: In *JABES*
+publication_types:
+- "2"
+selected: true
+title: "Liu F., Wang C.,  and Liu P.* (2015). A Semi-parametric Bayesian Approach for Differential Expression Analysis of RNA-seq Data. Journal of Agricultural, Biological, and Environmental Statistics. 20(4): 555-576."
+url_code: ''
+url_custom:
+- name: Link
+  url: https://link.springer.com/article/10.1007/s13253-015-0227-0
+url_dataset: ''
+url_pdf: 'https://link.springer.com/article/10.1007/s13253-015-0227-0'
+url_project: ''
+url_slides: ''
+url_video: ''
+---
+

content/publication/JCN2017.md

@@ -25,7 +25,7 @@ publication_short: In *JCN*
 publication_types:
 - "2"
 selected: true
-title: Single cell transcriptome profiling of developing chick retinal cells
+title: "Laboissonniere L. A., Martin G. M., Goetz J. J., Bi R., Pope B., Weinand K., Ellson L., Fru D., Lee M., Wester A. K., Liu P., Trimarchi J. M. (2017). Single cell transcriptome profiling of developing chick retinal cells. J Comp Neurol. 2017 Aug 15; 525(12): 2735-2781."
 url_code: ''
 url_custom:
 - name: Link

content/student.md

@@ -0,0 +1,27 @@
+---
+autolink: true
+date: 2018-03-20T00:00:00
+draft: false
+subtitle: ""
+title: 
+weight: 60
+widget: student
+---
+
+# Current Students
+### PhD students
+1. **[Emily Goren](http://emilygoren.github.io/)**. [<i class="fa fa-github-alt" style="color:#03396c;font-size:80%;padding-top:6px;"></i>](https://github.com/emilygoren)
+2. **Ran Bi**. [<i class="fa fa-github-alt" style="color:#03396c;font-size:80%;padding-top:6px;"></i>](https://github.com/biran1990)
+
+### MS students
+
+
+# Graduated Students
+### PhD students
+1. **Fangfang Liu**, *Statistical methods in detecting differential expressed genes, analyzing insertion tolerance for genes and group selection for survival data*, 2015. Now Manager of Statistics at Pfizer. 
+2. **Yaqing Si**, *Statistical analysis of RNA-seq data*, 2012. Now Associate Professor at Southwestern University of Finance and Economics.
+3. **Megan Orr** (Co-Major Professor: Dan Nettleton), *Assessing differential expression when the distribution of effect sizes is asymmetric and evaluating concordance of differential expression across multiple gene expression experiments*, 2012. Now a tenure-track Assistant Professor at North Dakota State University.
+4. **[Tieming Ji](http://faculty.missouri.edu/~jit/)** (Co-Major Professor: Dan Nettleton, Pat Schnable), *Borrowing information across genes and experiments for improved error variance estimation in microarray data analysis and statistical inferences for gene expression heterosis*, 2011. Now a tenure-track Assistant Professor at University of Missouri.
+
+### MS students
+1. **[William Landau](https://wlandau.github.io/)**, *Dispersion Estimation and Its Effect on Test Performance in RNA-seq Data Analysis: A Comparison of Methods*, 2013. Now Research Scientist at Eli Lilly and Company. [<i class="fa fa-github-alt" style="color:#03396c;font-size:80%;padding-top:6px;"></i>](https://github.com/wlandau)

content/talk/ICSA2012.md

@@ -0,0 +1,25 @@
+---
+date: 2012-06-23
+title: "An optimal test with maximum average power while controlling FDR with application to RNAseq
+data"
+abstract: The recent RNA-seq technology is an attractive method to study gene expression. One of the most important goals in RNA-seq data analysis is to detect genes differentially expressed across treatments. Although several statistical methods have been published, there are no theoretical justifications for whether these methods are optimal or how to search for the optimal test. Furthermore, most proposed tests are designed for testing whether the mean expression levels are exactly the same or not across treatments, whereas sometimes, biologists are interested in detecting genes with expression changes larger than a certain threshold. Another issue with current methods is that the false discovery rate (FDR) control is not well studied. In this manuscript, we propose a test to address all the above issues. Under model assumptions, we derive an optimal test that achieves the maximum of average power among those that control FDR at the same level. We also provide an approximated version, the approximated most average powerful (AMAP) test, for practical implementation. The proposed method allows for testing null hypotheses that are much more general than the ones most previous studies have considered, and it leads to a natural way of controlling the FDR. Through simulation studies, we show that our test has a higher power than other methods, including the widely-used edgeR, DESeq, and baySeq methods, as well as better FDR control than two other FDR control procedures commonly used in practice. For demonstration, we also apply the proposed method to a real RNA-seq dataset obtained from maize.
+abstract_short: ""
+event: 'ICSA Applied Statistics Symposium'
+event_url: ''
+location: 'Boston, Massachusetts, USA'
+header:
+  caption: 'An optimal test with maximum average power while controlling FDR with application to RNAseq
+data'
+  image: ''
+selected: true
+math: true
+url_code: ''
+url_custom: 
+# - name: Link
+#   url: ''
+url_dataset: ''
+url_pdf: ''
+url_project: ''
+url_slides: ''
+url_video: ''
+---

content/talk/JSM2013.md

@@ -0,0 +1,23 @@
+---
+date: 2013-08-07
+title: "A Novel Bayesian Approach for Differential Gene Expression Analysis with RNA-seq Data"
+abstract: RNA-sequencing (RNA-seq) technologies have revolutionized the way biologists study gene expression and generated tremendous amount of data waiting for analysis. Detecting differentially expressed genes is one of the fundamental steps in RNA-seq data analysis. We model the count expression data for each gene using a Poisson-Gamma hierarchical model, or equivalently, a negative binomial model. In this paper, we propose an optimal test using Dirichlet process mixture models for the parameter corresponding to the fold change between the two treatment means and conjugate priors for the other parameters in our model. We develop an inference strategy using collapsed Gibbs algorithm for differential expression analysis. Simulation results show our method is promising.
+abstract_short: ""
+event: 'Joint Statistical Meetings'
+event_url: 'https://ww2.amstat.org/meetings/jsm/2013/program.cfm'
+location: 'Montréal, Québec, CANADA'
+header:
+  caption: 'A Novel Bayesian Approach for Differential Gene Expression Analysis with RNA-seq Data'
+  image: ''
+selected: true
+math: true
+url_code: ''
+url_custom: 
+ - name: Link
+   url: 'https://ww2.amstat.org/meetings/jsm/2013/onlineprogram/AbstractDetails.cfm?abstractid=309751'
+url_dataset: ''
+url_pdf: ''
+url_project: ''
+url_slides: '/talk/JSM2013.pdf'
+url_video: ''
+---

content/talk/_index.md

@@ -0,0 +1,10 @@
+---
+date: 2017-01-01T00:00:00Z
+header:
+  caption: ""
+  image: ""
+highlight: false
+list_format: 0
+math: false
+title: Talks
+---